The PDC [Bypass] button doesn't 'turn off' PDC per se; it disables compensation only on Input-monitored tracks, which include synth tracks. Other tracks and the metronome are still delayed to sync with the track/bus that has the delay-inducing plugin on it), so any MIDI you record will be laid down late since you're playing to a delayed click. Audio recording, on the other hand, gets compensated for the added latency after the fact so it will sync on playback when input monitoring is disabled and/or PDC bypass is disengaged.